Yves Van de Peer - Ghent University/VIB 30 - 31 August 2018. Gent-Zwijnaarde, Belgium. IPBO conference 2018: “Scientific innovation for a sustainable development of African agriculture”

1. Yves Van de Peer
Ghent University/VIB
The African
Orphan
Crops
Consortium

2. The African
Orphan
Crops
Consortium
http://africanorphancrops.org

3. Growing Africa Out of Stunting, Hunger &
Malnutrition: The African Orphan Crops
Consortium
• Provide genomic tools to accelerate breeding in crops important to
African diets
• Train African plant breeders to use the latest strategies and
technologies in plant breeding
Make nutritious crops productive
Benefit comes through plant breeders

4. 37%
48%
7%
Stunting: Physical, Neurological, Economic
Stunting is the impaired
growth and development
that children experience
from poor nutrition.
Children are defined as
stunted if their height-for-
age is more than two
standard deviations below
the WHO Child Growth
Standards median.

5. It is not so
much a
question of
more food
It is more a
question of
better food
Stunting: Physical, Neurological, Economic

6. Founding members
New Partnership for Africa’s
Development (NEPAD)
Administration and development of
the AOCC
World Agroforestry Centre (ICRAF)
Incorporate AOCC species into its
agroforestry delivery vehicles such as
portfolio of (fruit) crops and
popularize them at local level and re-
sequence 100 accessions each from
the 101 species
Mars Inc.
African Plant Breeding Academy
scholarships for breeding programs
and support for AOCC lab personnel
World Wildlife Fund (WWF)
Endorse AOCC’s recommendations
and help raise support and
translation at country and
international level
University of California,
Davis (UC Davis)
Conceptualization,
technical guidance and
knowledge partner

7. Allen Van Deynze, PhD
Director of Research The Seed Biotechnology Center
Department of Plant Sciences, The University of California Davis
Steering Committee of the African Orphan Crops
Howard-Yana Shapiro, PhD
Chief Agricultural Officer, Mars, Incorporated
Fellow Mars Advanced Research Institute
Senior Fellow Plant Sciences, The University of California, Davis
Science Advisor, MIT Media Lab
Distinguished Fellow, The World Agroforestry Centre
Growing Africa Out of Stunting, Hunger &
Malnutrition: The African Orphan Crops
Consortium

8. Prasad Hendre
AOCC/ICRAF
Alice Muchugi
GRU/ICRAF
Ramni Jamnadass
ICRAF
Allen Van Deynze
UC Davis
Robert Kariba
AOCC/ICRAF
Samuel Muthemba
AOCC/ICRAF
Nelly Mutio
AOCC administrator
Albert Mwangi
AOCC website admin
John Innocent
AOCC website technician
Everyday governance …
The AOCC team
http://africanorphancrops.org

9. Uncommon Collaboration

10. The consortium’s goal is to sequence, assemble and annotate the genomes of
101 traditional African food crops, which will enable higher nutritional content
for society over the decades to come. The resulting information will be put in
the public domain with the endorsement of the African Union.
Sequence genetic diversity of 101 species x 100 lines
Main Goal 1!

11. List of African Orphan Crops to be sequenced

12. 28 orders
45 families
101 species
African Orphan Crops to be sequenced

13. A diverse panel of 100
scientists, anthropologists,
food scientists, nutritionists
and plant breeders, responded
to the survey.
Data rich survey on the key orphan crops,
distributed across Africa. These crops
represent the basic food system in rural Africa
The criteria for selecting the crops
included:
• Nutritional value
• Widespread use
• Not currently sequenced
• Climatic adaptability
• Drought & pest resistance
How were the crops chosen?

14. Six-week continuing education program for scientists in
crop improvement
• Review foundational principles of genetics, experimental
design/ statistics, plant breeding
• Share proven technologies that enhance genetic gains and
speed development of improved varieties
• Provide tools
• Model implementation through actual breeding programs
• Final thesis: critiqued by class and instructors
Located at ICRAF in Nairobi, Kenya, the Academy
will train 250 plant breeders and technicians in genomics
and marker-assisted selection for crop improvement
Main Goal 2: African Plant Breeding Academy!

15. Cohorts I,II,III comprised 80 scientists
representing 25 countries across the
African continent
• 67 PhD / 13 MSc
• 29 women
• > 91 crops
Theophile Ndacyayisenga
Rwanda
Wonder Nunekpeku, Ph.D.
Ghana
Godson
potato, sorghum cassava, pepper cow
Meet the students …

16. Outcomes and impact …
• 250 scientists and technicians empowered
• Trainers trained (sustainability)
• Professional networks formed and Communities of Practice developed
• New research funding garnered (> $18M by breeders)
• Improved crop varieties to underpin African food systems
• Key milestone in a Green Revolution for Africa!

17. De novo sequencing and resequencing …
Sequence
genetic diversity
of 101 species
x 100 lines

18. Species name Reference genome
Re-
sequencing Transcriptome Species name Reference genome
Re
sequencing Transcriptome
1 Eleusine coracana Final assembly On going Completed 31 Anacardium occidentale ON Yet to begin On going
2 Lablab purpureus Final assembly Yet to begin Completed 32 Dovyalis caffra On going Yet to begin Completed
3 Digitaria exilis Final assembly Yet to begin Yet to begin 33 Parinari curatellifolia On going On going Yet to begin
4 Solanum aethiopicum Final assembly Yet to begin Completed 34 Parkia biglobosa ON Yet to begin ON
5 Cleome gynandra Draft assembly ON ON 35 Saba comorensis ON Yet to begin Yet to begin
6 Vigna subterranea Final assembly ON Completed 36 Uapaca kirkiana ON ON ON
7 Celosia argentea ON Yet to begin Completed 37 Elaeis guineensis Non-BGI Yet to begin Non-BGI
8 Phaseolus vulgaris ON ON Yet to begin 38 Mangifera indica Non-BGI Yet to begin Non-BGI
9 Solanum nigrum ON Yet to begin ON 39 Macadamia ternifolia Non-BGI Yet to begin Non-BGI
10 Brassica carinata Non-BGI ON Non-BGI 40 Persea americana Non-BGI Yet to begin Non-BGI
11 Lens culinaris Non-BGI Yet to begin Non-BGI 41 Casimiroa edulis ON Yet to begin Completed
12 Allium cepa Non-BGI Yet to begin Non-BGI 42 Dacryodes edulis ON Yet to begin ON
13 Amaranthus tricolor Non-BGI Yet to begin Non-BGI 43 Vitellaria paradoxa ON Yet to begin Yet to begin
14 Carica papaya Non-BGI Yet to begin Non-BGI 44 Ziziphus mauritiana ON Yet to begin ON
15 Citrullus lanatus Non-BGI Yet to begin Non-BGI 45 Tamarindus indica ON Yet to begin Tissue collected
16 Cucurbita maxima Non-BGI Yet to begin Non-BGI 46 Syzygium guineense ON Yet to begin Tissue collected
17 Dioscorea alata Non-BGI Yet to begin Non-BGI 47 Irvingia gabonensis DNA Yet to begin Yet to begin
18 Dioscorea dume torum Non-BGI Yet to begin Non-BGI 48 Ricinodendron heudelotii DNA Yet to begin Tissue collected
19 Erogrostis tef Non-BGI Yet to begin Non-BGI 49 Detarium microcarpum ON Yet to begin Yet to begin
20 Ipomoea batatas Non-BGI Yet to begin Non-BGI 50 Garcinia livingstonei ON Yet to begin Yet to begin
21 Musa acuminata AAA Group Non-BGI Yet to begin Non-BGI 51 Vitex doniana Yet to begin Yet to begin Tissue collected
22 Momordica charantia Non-BGI Yet to begin Non-BGI 52 Allanblackia stulhmanli Yet to begin Yet to begin Tissue collected
23 Annona senegalensis. Final assembly Yet to begin Completed 53 Strychnos cocculoides Yet to begin ON ON
24 Artocarpus heterophyllus Final assembly Yet to begin Completed 54 Strychnos spinosa Yet to begin Yet to begin Tissue collected
25 Faidherbia albida Final assembly Yet to begin Completed 55 Annona reticulata Yet to begin Yet to begin Tissue collected
26 Sclerocarya birrea Final assembly Yet to begin ON 56 Vangueria madagascariensis Yet to begin Yet to begin ON
27 Moringa oleifera Final assembly Yet to begin Completed 57 Passiflora edulis Yet to begin Yet to begin Non-BGI
28 Artocarpus altilis Final assembly Yet to begin Completed 58 Psidium guajava Non-BGI Yet to begin Non-BGI
29 Adansonia digitata ON 5 received Tissue collected 59 Morus alba Non-BGI Yet to begin Non-BGI
30 Adansonia kilima ON Yet to begin Tissue collected

19. Summary of the genome survey
Of the 29 species sequenced
• Genome sizes range from 280 Mb to 2.9 Gb
• 5 species have relatively simple genomes
• 7 species are highly heterozygous
• 8 species have high repeat content
• Some species are tetraploid

20. Pentapetalae
Fabids
Asterids
Lamiids
Malvids
Mesangiospermae
Fabaceae
Organism
Estimated
Genome size
Ploidy
Heter/
Homozygous
Genome
survey
Lablab purpureus 0.43 Gb 2X Homo Normal
Vigna subterranee 0.51 Gb 2X Homo Normal
Tamarindus indica 1.67 Gb 2X Homo Normal
Detarium microcarpum 0.53 Gb 4X Heter HH
Faidherbia albida 0.66 Gb 2X Heter HH
Parkia biglobosa ND ND ND ND
Artocarpus altilis 0.80 Gb 2X Homo RR&HH
Artocarpus heterophyllus 1.01 Gb 2X Homo RR&HH
Ziziphus mauritiana ND ND ND ND
Dovyalis caffra 0.44 Gb 2X Homo Normal
Parinari curatefolia ND ND ND ND
Garcinia livingstonei ND ND ND ND
Uapaca kirkiana ND ND ND ND
Casmiroa dulis 1.21 Gb 4X Homo RR
Sclerocarya birrea 0.37 Gb 2X Heter HH
Dacryodes edulis 0.74 Gb 4X Homo HH
Adansonia digitata 2.9 Gb 4X Heter --
Adansonia kilima 2.9 Gb 4X Heter --
Moringa oleifera 0.28 Gb 2X Heter RR&HH
Syzygium guineense ND ND ND ND
Solanum nigrum ND ND ND ND
Solanum aethicopicum 1.17 Gb 2X Homo RR
Saba senegalensis ND ND ND ND
Vitellaria paradoxa ND ND ND --
Celosia argentea 2.1 Gb 2X Homo Normal
Elusine coracana 1.29 Gb 4X Homo RR
Elusine indica 1.23 Gb 2X Homo RR
Digitaria exilis 0.71 Gb 2X Homo RR
Annona senegalensis 0.74 Gb 2X Homo RR
Notes：
HH：Highly heterozygous
RR：Repeat-rich
Poaceae
Salicaceae
Clusiaceae
Chrysobalanaceae
Malvaceae
Myrtaceae
Moringaceae
Burseraceae
Solanaceae
Apocynaceae
Sapotaceae
Amaranthaceae
Annonaceae
Rhamnaceae
Moraceae
Phyllanthaceae
Rosales
Malpighiales
Sapindales
Fabales
Rutaceae
Rosids
The 29 genomes
sequenced …

21. 49 other genomes
are currently being
worked on
The 10 species with
genomes
assembled …

22. • Plants
• Poplar tree (Science)
• Vitis vinifera (PLoS One)
• Arabidopsis lyrata (Nature Genetics)
• Malus domestica (Nature Genetics)
• Medicago truncatula (Nature)
• Solanum lycopersicum (Nature)
• Picea abies (spruce) (Nature)
• Physcomitrella patens (moss) (Science)
• Eucalyptus grandis (Nature)
• Phalaenopsis (orchid) (Nature Genetics)
• Zostera marina (Nature)
• Apostasia (orchid) (Nature)
• Algae
• Ostreococcus (PNAS)
• Micromonas (Science)
• the brown alga Ectocarpus siliculosus (Nature)
• Emiliana huxleyi (Nature)
Involvement of UGent/VIB

23. RFAM Repeats
454
SOLiD
Illumina
ESTs
Genome
sequence
RepeatMasker
Infernal
GenomethreaderBowtie/Tophat
TAIR10
UNIPROT
SWISSP
BLASTX
AUGUSTUS GlimmerGeneID TwinScan GeneMark
EUGENE
Proteins
BLASTP
INTERPRO-scan
SifterGO
Best-hit
Text Mining
Human readable functional
description
OrthoMCL
Gene
Families
Non-coding
genes
cDNA
CDS
Phylogeny
Gene
prediction
and
genome
annotation
pipeline

24. Online Resource
for Community
Annotation of
Eukaryotes
Online annotation tools

25. Moringa, the new superfood?

26. Moringa, the new superfood?

27. • Many parts of moringa are edible,
with regional uses varying widely:
• Immature seed pods, called "drumsticks"
• Leaves
• Mature seeds
• Oil pressed from seeds
• Flowers
Moringa oleifera, or drumstick tree

28. Finger Millet (Eleusine coracana)
• Indigenous to eastern Africa (but also widely
grown in India
• Adapted to diverse agro-ecologies
• Excellent source of nutrition for expectant
mothers and children
• Demand outstrips supply
• Challenges with pathogens

29. Mineral composition (mg/100g)
Ca Fe Mg K Cu Mn Zn
Finger millet 344 3.9 137 408 0.47 5.49 2.3
Wheat 41 3.9 120 363 0.9 13.3 1
Rice 10 0.5 32 130 0.25 1.1 1.2
Maize 10 2.3 0.163 270 0.22 0.163 0.46
Source: USDA database
Finger Millet (Eleusine coracana)
Nutritional quality
• High in unsaturated fatty acids, protein,
fibre, micronutrients
• Superior malting quality
• Gluten-free

30. Growth and Analysis of Diverse Cleome Lines
Deedi Sogbohossou and Enoch Achigan-Dako
University of Abomey-Calavi in Benin, Wageningen University
Cleome gynandra (spider plant)

31. Asian lines
Early flowering
Low carotenoids content
Rich in tocopherols
Light green leaves
African lines
Late flowering
Rich in carotenoids
Low levels of tocopherols
Dark green leaves
PCA based on carotenoids, tocopherols and flowering time in Cleome gynandra
Deedi Sogbohossou
Wageningen University
NWO-WOTTRO
Marker-assisted
selection could combine
the best traits of both
groups to improve
nutritional content.
Cleome gynandra (spider plant)

32. Acknowledgements
UC DAVIS
• Allen van Deynze
BGI
• Shifeng Cheng
• Yue Chang
• Yuan Fu
AOCC/ICRAF
• Prasad Hendre
• Ansie Yssel
• Lorenzo Carretero-Paulet
• Lieven Sterck
The entire AOCC